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r1162: fixed a typo; also increased splice pen 

Now slightly better on ISO-seq
This commit is contained in:
Heng Li 2023-04-07 01:19:18 -04:00
parent 1834b1fd42
commit ea2042a577
2 changed files with 14 additions and 14 deletions
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26
ksw2_exts2_sse.c
View File

@ -123,7 +123,7 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
int sp[4];
if (flag & KSW_EZ_SPLICE_CMPLX) {
for (t = 0; t < 4; ++t)
sp[t] = (int)((double)sp0[t] / 4. + .499);
sp[t] = (int)((double)sp0[t] / 3. + .499);
} else {
sp[0] = flag&KSW_EZ_SPLICE_FLANK? noncan / 2 : 0;
sp[1] = sp[2] = sp[3] = noncan;
@ -134,12 +134,12 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
for (t = 0; t < tlen - 4; ++t) {
int z = 3;
if (flag & KSW_EZ_SPLICE_FOR) {
if (target[t+1] == 2 && target[t+2] == 3) // |GT.
if (target[t+1] == 2 && target[t+2] == 3) // |GT.
z = target[t+3] == 0 || target[t+3] == 2? -1 : 0; // |GTr or not
else if (target[t+1] == 2 && target[t+2] == 1) z = 1; // |GC.
else if (target[t+1] == 0 && target[t+2] == 3) z = 2; // |AT.
} else if (flag & KSW_EZ_SPLICE_REV) {
if (target[t+1] == 1 && target[t+2] == 3) // |CT. (revcomp of .AG|)
if (target[t+1] == 1 && target[t+2] == 3) // |CT. (revcomp of .AG|)
z = target[t+3] == 0 || target[t+3] == 2? -1 : 0;
else if (target[t+1] == 2 && target[t+2] == 3) z = 2; // |GT. (revcomp of .AC|)
}
@ -148,13 +148,13 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
for (t = 2; t < tlen; ++t) {
int z = 3;
if (flag & KSW_EZ_SPLICE_FOR) {
if (target[t-1] == 0 && target[t] == 2) // .AG|
if (target[t-1] == 0 && target[t] == 2) // .AG|
z = target[t-2] == 1 || target[t-2] == 3? -1 : 0; // yAG| or not
else if (target[t-1] == 0 && target[t] == 1) z = 2; // .AC|
} else if (flag & KSW_EZ_SPLICE_REV) {
if (target[t-1] == 0 && target[t] == 1) // .AC| (revcomp of |GT.)
if (target[t-1] == 0 && target[t] == 1) // .AC| (revcomp of |GT.)
z = target[t-2] == 1 || target[t-2] == 3? -1 : 0; // yAC| or not
else if (target[t-1] == 1 && target[t] == 2) z = 1; // .CG| (revcomp of |GC.)
else if (target[t-1] == 2 && target[t] == 1) z = 1; // .GC| (revcomp of |GC.)
else if (target[t-1] == 0 && target[t] == 3) z = 2; // .AT| (revcomp of |AT.)
}
((int8_t*)acceptor)[t] = z < 0? 0 : -sp[z];
@ -163,11 +163,11 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
for (t = 0; t < tlen - 4; ++t) {
int z = 3;
if (flag & KSW_EZ_SPLICE_FOR) {
if (target[t+1] == 2 && target[t+2] == 0) // |GA. (rev of .AG|)
if (target[t+1] == 2 && target[t+2] == 0) // |GA. (rev of .AG|)
z = target[t+3] == 1 || target[t+3] == 3? -1 : 0;
else if (target[t+1] == 1 && target[t+2] == 0) z = 2; // |CA. (rev of .AC|)
} else if (flag & KSW_EZ_SPLICE_REV) {
if (target[t+1] == 1 && target[t+2] == 0) // |CA. (comp of |GT.)
if (target[t+1] == 1 && target[t+2] == 0) // |CA. (comp of |GT.)
z = target[t+3] == 1 || target[t+3] == 3? -1 : 0;
else if (target[t+1] == 1 && target[t+2] == 2) z = 1; // |CG. (comp of |GC.)
else if (target[t+1] == 3 && target[t+2] == 0) z = 2; // |TA. (comp of |AT.)
@ -177,14 +177,14 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
for (t = 2; t < tlen; ++t) {
int z = 3;
if (flag & KSW_EZ_SPLICE_FOR) {
if (target[t-1] == 3 && target[t] == 2) // .TG| (rev of |GT.)
if (target[t-1] == 3 && target[t] == 2) // .TG| (rev of |GT.)
z = target[t-2] == 0 || target[t-2] == 2? -1 : 0;
else if (target[t-1] == 1 && target[t] == 2) z = 1; // .CG|
else if (target[t-1] == 3 && target[t] == 0) z = 2; // .TA|
else if (target[t-1] == 1 && target[t] == 2) z = 1; // .CG| (rev of |GC.)
else if (target[t-1] == 3 && target[t] == 0) z = 2; // .TA| (rev of |AT.)
} else if (flag & KSW_EZ_SPLICE_REV) {
if (target[t-1] == 3 && target[t] == 1) // .TC| (comp of .AG|)
if (target[t-1] == 3 && target[t] == 1) // .TC| (comp of .AG|)
z = target[t-2] == 0 || target[t-2] == 2? -1 : 0;
else if (target[t-1] == 3 && target[t] == 2) z = 2; // .TG|
else if (target[t-1] == 3 && target[t] == 2) z = 2; // .TG| (comp of .AC|)
}
((int8_t*)acceptor)[t] = z < 0? 0 : -sp[z];
}

2
minimap.h
View File

@ -5,7 +5,7 @@
#include <stdio.h>
#include <sys/types.h>
#define MM_VERSION "2.24-r1161-dirty"
#define MM_VERSION "2.24-r1162-dirty"
#define MM_F_NO_DIAG 0x001 // no exact diagonal hit
#define MM_F_NO_DUAL 0x002 // skip pairs where query name is lexicographically larger than target name